Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002464.1 Hibiscus syriacus cultivar Beakdansim tig00005040_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 66417
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:1127 original size:20 final size:20
Alignment explanation
Indices: 1097--1144 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
1087 TCCTACTAGA
1097 AGTAT-GATACTCTACCCTC
1 AGTATCGATACTCTACCCTC
1116 AGTATCGATACTCTACCCTC
1 AGTATCGATACTCTACCCTC
*
1136 ATTATCGAT
1 AGTATCGAT
1145 CCCTTAAGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 5 0.19
20 22 0.81
ACGTcount: A:0.27, C:0.29, G:0.10, T:0.33
Consensus pattern (20 bp):
AGTATCGATACTCTACCCTC
Found at i:2657 original size:23 final size:23
Alignment explanation
Indices: 2631--2675 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2621 TATAAATGAA
* *
2631 GTTCGTGAACATTAAACAAACAT
1 GTTCATGAACAATAAACAAACAT
*
2654 GTTCATGAACAATAAATAAACA
1 GTTCATGAACAATAAACAAACA
2676 AACATGAACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.49, C:0.16, G:0.11, T:0.24
Consensus pattern (23 bp):
GTTCATGAACAATAAACAAACAT
Found at i:13366 original size:68 final size:66
Alignment explanation
Indices: 13265--13390 Score: 189
Period size: 68 Copynumber: 1.9 Consensus size: 66
13255 TTTAAATTAT
* * * *
13265 AATTTTTAGACTATTTTTTTATTTTACATATTAAGTTGTATTTGAGTAGTTTGGTAAGGTAATAG
1 AATTATTAGACTATTTTTTTATTTTACAGATTAAATCGTATTTGAGTAGTTTGGTAAGGTAATAG
13330 A
66 A
*
13331 AATTATTAGACTATTTATTTTCATTTTACAGATTAAATCGTATTTGAGTGGTTTGGTAAG
1 AATTATTAGACTATTT-TTTT-ATTTTACAGATTAAATCGTATTTGAGTAGTTTGGTAAG
13391 TTTTATTTAA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
66 15 0.28
67 4 0.08
68 34 0.64
ACGTcount: A:0.30, C:0.05, G:0.17, T:0.48
Consensus pattern (66 bp):
AATTATTAGACTATTTTTTTATTTTACAGATTAAATCGTATTTGAGTAGTTTGGTAAGGTAATAG
A
Found at i:13476 original size:18 final size:19
Alignment explanation
Indices: 13442--13477 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
13432 ATTAATTAGA
13442 ATATTTATTTTGATTTAAC
1 ATATTTATTTTGATTTAAC
*
13461 ATATTTTTTTTG-TTTAA
1 ATATTTATTTTGATTTAA
13478 ATTTTCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.03, G:0.06, T:0.64
Consensus pattern (19 bp):
ATATTTATTTTGATTTAAC
Found at i:15615 original size:23 final size:23
Alignment explanation
Indices: 15589--15632 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
15579 ATATTAAATA
15589 AAATATTGATATTATCCACATAG
1 AAATATTGATATTATCCACATAG
*
15612 AAATATTGATATTATTCACAT
1 AAATATTGATATTATCCACAT
15633 TCATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.39
Consensus pattern (23 bp):
AAATATTGATATTATCCACATAG
Found at i:15686 original size:27 final size:27
Alignment explanation
Indices: 15656--15707 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
15646 ACATCAACAA
*
15656 ATATCCATCACATTCATTCAAATATTG
1 ATATCAATCACATTCATTCAAATATTG
* *
15683 ATATTAATCATATTCATTCAAATAT
1 ATATCAATCACATTCATTCAAATAT
15708 AACATCAACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.40, C:0.17, G:0.02, T:0.40
Consensus pattern (27 bp):
ATATCAATCACATTCATTCAAATATTG
Found at i:18610 original size:19 final size:18
Alignment explanation
Indices: 18578--18625 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
18568 GGTAAAAATT
* *
18578 AAAATTATACTTATGACGA
1 AAAATTAAATTTATGA-GA
**
18597 AAAATTAAATTTATGATT
1 AAAATTAAATTTATGAGA
18615 AAAATTAAATT
1 AAAATTAAATT
18626 AATTAATTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 11 0.44
19 14 0.56
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (18 bp):
AAAATTAAATTTATGAGA
Found at i:18648 original size:27 final size:24
Alignment explanation
Indices: 18618--18672 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
18608 TATGATTAAA
*
18618 ATTAAATTAATTAATTACTAAAATATT
1 ATTAAATTAATT-A-TAAT-AAATATT
*
18645 ATTAATTTAATTATAATAAATATT
1 ATTAAATTAATTATAATAAATATT
18669 ATTA
1 ATTA
18673 GAGTTACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 11 0.42
25 3 0.12
26 1 0.04
27 11 0.42
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
ATTAAATTAATTATAATAAATATT
Found at i:18761 original size:47 final size:47
Alignment explanation
Indices: 18707--18801 Score: 154
Period size: 47 Copynumber: 2.0 Consensus size: 47
18697 TAAAAATATT
* *
18707 TTTTAACATTTTTACTAGAAATACTAAATCAAATGTTGATCTAATTA
1 TTTTAACATTTTTACTAGAAATACTAAATCAAATATTGATCAAATTA
* *
18754 TTTTAACATTTTTACTAGAAATATTAAATCAAATATTTATCAAATTA
1 TTTTAACATTTTTACTAGAAATACTAAATCAAATATTGATCAAATTA
18801 T
1 T
18802 ACTAATGATT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.44
Consensus pattern (47 bp):
TTTTAACATTTTTACTAGAAATACTAAATCAAATATTGATCAAATTA
Found at i:18893 original size:24 final size:24
Alignment explanation
Indices: 18847--18893 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
18837 CTAATGACGA
* * *
18847 AAAATTAAATTTATGATTTAAATT
1 AAAATTAAATTAATGACTAAAATT
*
18871 AAAATTAAATTAATTACTAAAAT
1 AAAATTAAATTAATGACTAAAAT
18894 ATTATTAAAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (24 bp):
AAAATTAAATTAATGACTAAAATT
Found at i:19113 original size:22 final size:24
Alignment explanation
Indices: 19058--19114 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
19048 CTATTGAGGT
19058 TATTATTTTTCGTCATTATAATAAA
1 TATT-TTTTTCGTCATTATAATAAA
* *
19083 TATTATTTTTTGTCATTATAAT-TA
1 TATT-TTTTTCGTCATTATAATAAA
19107 TATTTTTT
1 TATTTTTT
19115 AACATTTCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 4 0.13
24 5 0.17
25 21 0.70
ACGTcount: A:0.30, C:0.05, G:0.04, T:0.61
Consensus pattern (24 bp):
TATTTTTTTCGTCATTATAATAAA
Found at i:21806 original size:21 final size:21
Alignment explanation
Indices: 21780--21819 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
21770 AGCAAAACAG
* *
21780 TGCTGAATGATTTAGCACATT
1 TGCTGAATCAATTAGCACATT
21801 TGCTGAATCAATTAGCACA
1 TGCTGAATCAATTAGCACA
21820 GAAGTACATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (21 bp):
TGCTGAATCAATTAGCACATT
Found at i:28277 original size:25 final size:25
Alignment explanation
Indices: 28249--28298 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
28239 GTTTTTAGTA
*
28249 AACACGTCTTCTTTCAAATCGATGG
1 AACACGTCTTCATTCAAATCGATGG
28274 AACACGTCTTCATTCAAATCGATGG
1 AACACGTCTTCATTCAAATCGATGG
28299 GGGAAACAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (25 bp):
AACACGTCTTCATTCAAATCGATGG
Found at i:34158 original size:21 final size:22
Alignment explanation
Indices: 34133--34179 Score: 87
Period size: 21 Copynumber: 2.2 Consensus size: 22
34123 TCCACCGTTA
34133 ATTATTTTAATTTAAAC-AAAT
1 ATTATTTTAATTTAAACTAAAT
34154 ATTATTTTAATTTAAACTAAAT
1 ATTATTTTAATTTAAACTAAAT
34176 ATTA
1 ATTA
34180 CGGTTAGAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTATTTTAATTTAAACTAAAT
Found at i:35329 original size:12 final size:13
Alignment explanation
Indices: 35293--35336 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
35283 GCCCCGATTA
35293 CCCGATTACCCGC
1 CCCGATTACCCGC
35306 CCCGATTACCCGC
1 CCCGATTACCCGC
*
35319 CCCGA-TACCCGA
1 CCCGATTACCCGC
35331 CCCGAT
1 CCCGAT
35337 AAATATTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.18, C:0.52, G:0.16, T:0.14
Consensus pattern (13 bp):
CCCGATTACCCGC
Found at i:35475 original size:12 final size:12
Alignment explanation
Indices: 35460--35494 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
35450 CGATTCTCGG
35460 CCCAATACCCGA
1 CCCAATACCCGA
*
35472 CCCAATACCCGG
1 CCCAATACCCGA
35484 CCCAATACCCG
1 CCCAATACCCG
35495 TTTAAATAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.29, C:0.51, G:0.11, T:0.09
Consensus pattern (12 bp):
CCCAATACCCGA
Found at i:35698 original size:30 final size:30
Alignment explanation
Indices: 35662--35719 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
35652 CCATCCCTAC
* * *
35662 ATAGGTCTTCAGGAGCACATGGCGACCTCT
1 ATAGGTCTCCAGAAGCACACGGCGACCTCT
*
35692 ATAGGTCTCCATAAGCACACGGCGACCT
1 ATAGGTCTCCAGAAGCACACGGCGACCT
35720 ATGGAACTGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.24, T:0.21
Consensus pattern (30 bp):
ATAGGTCTCCAGAAGCACACGGCGACCTCT
Found at i:35808 original size:19 final size:19
Alignment explanation
Indices: 35784--35828 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
35774 TGTCACAAGT
35784 AGCACTTAGCGATCTATGG
1 AGCACTTAGCGATCTATGG
35803 AGCACTTAGCGATCTATGG
1 AGCACTTAGCGATCTATGG
35822 AGCACTT
1 AGCACTT
35829 GGTGACCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (19 bp):
AGCACTTAGCGATCTATGG
Found at i:46531 original size:27 final size:26
Alignment explanation
Indices: 46483--46533 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
46473 ATTTCCCCTC
* *
46483 CCCTTCGCCAGTGCTCTTCCATCATT
1 CCCTTCGCCAGAGCTCTCCCATCATT
*
46509 CCCTTCGCCCGAGCTCTCCCCATCA
1 CCCTTCGCCAGAGCTCT-CCCATCA
46534 ACCTCATGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 15 0.71
27 6 0.29
ACGTcount: A:0.12, C:0.49, G:0.12, T:0.27
Consensus pattern (26 bp):
CCCTTCGCCAGAGCTCTCCCATCATT
Found at i:46858 original size:31 final size:30
Alignment explanation
Indices: 46820--46910 Score: 130
Period size: 31 Copynumber: 2.9 Consensus size: 30
46810 AACGCCAGGC
46820 ACCTAAAATAGTAATAGAGAAAACGTTAAGA
1 ACCTAAAATAGTAATAG-GAAAACGTTAAGA
*
46851 ACCTAAAATAGTATTATGGAAAACGTTAAGA
1 ACCTAAAATAGTAATA-GGAAAACGTTAAGA
46882 ACCTAAAATAGTTACAT-GGAAAACGTTAA
1 ACCTAAAATAG-TA-ATAGGAAAACGTTAA
46911 ACACCGAGAT
Statistics
Matches: 55, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
31 51 0.93
32 3 0.05
33 1 0.02
ACGTcount: A:0.51, C:0.11, G:0.15, T:0.23
Consensus pattern (30 bp):
ACCTAAAATAGTAATAGGAAAACGTTAAGA
Found at i:47660 original size:4 final size:4
Alignment explanation
Indices: 47651--47676 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
47641 ATAATATTTG
47651 ATTA ATTA ATTA ATTA ATTA ATTA AT
1 ATTA ATTA ATTA ATTA ATTA ATTA AT
47677 GATCTCGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:50931 original size:28 final size:28
Alignment explanation
Indices: 50891--50962 Score: 144
Period size: 28 Copynumber: 2.6 Consensus size: 28
50881 TCAACCATTT
50891 GTGCAACTTCAATTATCTTAAAATGCTA
1 GTGCAACTTCAATTATCTTAAAATGCTA
50919 GTGCAACTTCAATTATCTTAAAATGCTA
1 GTGCAACTTCAATTATCTTAAAATGCTA
50947 GTGCAACTTCAATTAT
1 GTGCAACTTCAATTAT
50963 TTTTTTTCGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (28 bp):
GTGCAACTTCAATTATCTTAAAATGCTA
Found at i:51335 original size:41 final size:43
Alignment explanation
Indices: 51263--51346 Score: 102
Period size: 41 Copynumber: 2.0 Consensus size: 43
51253 ATATCATAAT
* *
51263 ATTATATAAATAAGTTCAATTAAATTTTTTTAAA-AATTAAAATTA
1 ATTAAATAAATAAGTTCAAATAAA--TTTTTAAATAA-TAAAATTA
51308 ATTAAATAAA-AAGTTCAAATAAA-TTTTAAATAATAAAAT
1 ATTAAATAAATAAGTTCAAATAAATTTTTAAATAATAAAAT
51347 AATACACATT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
41 13 0.36
42 2 0.06
44 12 0.33
45 9 0.25
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (43 bp):
ATTAAATAAATAAGTTCAAATAAATTTTTAAATAATAAAATTA
Found at i:51821 original size:20 final size:21
Alignment explanation
Indices: 51782--51824 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
51772 CAAGCTAAAT
51782 GCTGAACGGTTCAACATTAAGA
1 GCTGAACGGTTC-ACATTAAGA
*
51804 GCTGAATGGTTC-CATTAAGA
1 GCTGAACGGTTCACATTAAGA
51824 G
1 G
51825 GCAAACAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
22 11 0.55
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.26
Consensus pattern (21 bp):
GCTGAACGGTTCACATTAAGA
Found at i:51996 original size:17 final size:17
Alignment explanation
Indices: 51976--52010 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
51966 ATATACAAAT
51976 TACAAAATCAACCATCC
1 TACAAAATCAACCATCC
51993 TACAAAATCAACCATCC
1 TACAAAATCAACCATCC
52010 T
1 T
52011 CTGAGTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.34, G:0.00, T:0.20
Consensus pattern (17 bp):
TACAAAATCAACCATCC
Found at i:54677 original size:24 final size:24
Alignment explanation
Indices: 54650--54695 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
54640 TTTATAATTA
54650 TCCTTTATTTAAATTAATTCATAC
1 TCCTTTATTTAAATTAATTCATAC
54674 TCCTTTATTTAAATTAATTCAT
1 TCCTTTATTTAAATTAATTCAT
54696 TCTTGTACCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.52
Consensus pattern (24 bp):
TCCTTTATTTAAATTAATTCATAC
Found at i:55370 original size:22 final size:21
Alignment explanation
Indices: 55321--55362 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
55311 GAGTTCTATT
* *
55321 AAAATAATATTTATTTTTTAA
1 AAAATAAAAATTATTTTTTAA
55342 AAAATAAAAATTATTTTTTAA
1 AAAATAAAAATTATTTTTTAA
55363 TTATATAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
AAAATAAAAATTATTTTTTAA
Found at i:55781 original size:14 final size:14
Alignment explanation
Indices: 55762--55790 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
55752 CTAACAATAT
55762 AAGAAAGTATTTTA
1 AAGAAAGTATTTTA
55776 AAGAAAGTATTTTA
1 AAGAAAGTATTTTA
55790 A
1 A
55791 GGATAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (14 bp):
AAGAAAGTATTTTA
Found at i:61817 original size:51 final size:51
Alignment explanation
Indices: 61757--61975 Score: 286
Period size: 51 Copynumber: 4.4 Consensus size: 51
61747 AAAAATATAG
*
61757 CACTTAACACATGCTTACACTGGTGTAAGTGAATAAAATAAACAAGTGTAA
1 CACTTAACACATACTTACACTGGTGTAAGTGAATAAAATAAACAAGTGTAA
* * *
61808 CACTGAACACATACTTACACCGGTGTAAGTGAATAAAATAAACAAGTGTAG
1 CACTTAACACATACTTACACTGGTGTAAGTGAATAAAATAAACAAGTGTAA
* * * *
61859 CACTCAACATATACTT-TACTGGTATAAGTGAAT--AA-AAA-AAGTGTAA
1 CACTTAACACATACTTACACTGGTGTAAGTGAATAAAATAAACAAGTGTAA
* * * *
61905 CACTTAACACATATTTACAATGGTGTAAGTAAATAAAATAAAAAAAGTGTAA
1 CACTTAACACATACTTACACTGGTGTAAGTGAATAAAAT-AAACAAGTGTAA
61957 CACTTAACACATACTTACA
1 CACTTAACACATACTTACA
61976 GCGATGTAAG
Statistics
Matches: 144, Mismatches: 18, Indels: 11
0.83 0.10 0.06
Matches are distributed among these distances:
46 20 0.14
47 16 0.11
48 2 0.01
49 2 0.01
50 14 0.10
51 64 0.44
52 26 0.18
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.26
Consensus pattern (51 bp):
CACTTAACACATACTTACACTGGTGTAAGTGAATAAAATAAACAAGTGTAA
Found at i:61914 original size:97 final size:101
Alignment explanation
Indices: 61743--61972 Score: 272
Period size: 97 Copynumber: 2.3 Consensus size: 101
61733 AAATCATATT
* * * * * *
61743 ATAAAAAAA-TATAGCACTTAACACATGCTTACACTGGTGTAAGTGAATAAAATAAACAAGTGTA
1 ATAAAAAAAGTGTAACACTCAACACATACTT-TACTGGTATAAGTGAAT-AAATAAACAAGTGTA
* *
61807 ACACTGAACACATACTTACACCGGTGTAAGTGAATAAA
64 ACACTGAACACATACTTACAACGGTGTAAGTAAATAAA
* * *
61845 AT-AAACAAGTGTAGCACTCAACATATACTTTACTGGTATAAGTGAAT-AA-AAA-AAGTGTAAC
1 ATAAAAAAAGTGTAACACTCAACACATACTTTACTGGTATAAGTGAATAAATAAACAAGTGTAAC
* * *
61906 ACTTAACACATATTTACAATGGTGTAAGTAAATAAA
66 ACTGAACACATACTTACAACGGTGTAAGTAAATAAA
*
61942 ATAAAAAAAGTGTAACACTTAACACATACTT
1 ATAAAAAAAGTGTAACACTCAACACATACTT
61973 ACAGCGATGT
Statistics
Matches: 110, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
97 42 0.38
98 27 0.25
99 2 0.02
101 20 0.18
102 19 0.17
ACGTcount: A:0.47, C:0.14, G:0.13, T:0.26
Consensus pattern (101 bp):
ATAAAAAAAGTGTAACACTCAACACATACTTTACTGGTATAAGTGAATAAATAAACAAGTGTAAC
ACTGAACACATACTTACAACGGTGTAAGTAAATAAA
Found at i:61984 original size:52 final size:51
Alignment explanation
Indices: 61743--61987 Score: 236
Period size: 51 Copynumber: 4.9 Consensus size: 51
61733 AAATCATATT
* * * *
61743 ATAAAAAAA-TATAGCACTTAACACATGCTTACACTGGTGTAAGTGAATAAA
1 ATAAAAAAAGTGTAACACTTAACACATACTTACAC-GGTGTAAGTAAATAAA
* * *
61794 AT-AAACAAGTGTAACACTGAACACATACTTACACCGGTGTAAGTGAATAAA
1 ATAAAAAAAGTGTAACACTTAACACATACTTACA-CGGTGTAAGTAAATAAA
* * * * * * * *
61845 AT-AAACAAGTGTAGCACTCAACATATACTT-TACTG-GT-A-TAAGT-GA
1 ATAAAAAAAGTGTAACACTTAACACATACTTACACGGTGTAAGTAAATAAA
* *
61890 ATAAAAAAAGTGTAACACTTAACACATATTTACAATGGTGTAAGTAAATAAA
1 ATAAAAAAAGTGTAACACTTAACACATACTTAC-ACGGTGTAAGTAAATAAA
*
61942 ATAAAAAAAGTGTAACACTTAACACATACTTACAGCGATGTAAGTA
1 ATAAAAAAAGTGTAACACTTAACACATACTTACA-CGGTGTAAGTA
61988 TGTACATCTC
Statistics
Matches: 158, Mismatches: 26, Indels: 19
0.78 0.13 0.09
Matches are distributed among these distances:
45 3 0.02
46 26 0.16
47 1 0.01
48 4 0.03
49 4 0.03
50 7 0.04
51 70 0.44
52 43 0.27
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.25
Consensus pattern (51 bp):
ATAAAAAAAGTGTAACACTTAACACATACTTACACGGTGTAAGTAAATAAA
Found at i:62790 original size:30 final size:29
Alignment explanation
Indices: 62722--62789 Score: 118
Period size: 30 Copynumber: 2.3 Consensus size: 29
62712 TGACCATACG
62722 TTTATTTTTGTTAAGTTTAGTACATAAAC
1 TTTATTTTTGTTAAGTTTAGTACATAAAC
*
62751 TATTATTTTTGTTAAGTTTGGTACATAAAC
1 T-TTATTTTTGTTAAGTTTAGTACATAAAC
62781 TTTATTTTT
1 TTTATTTTT
62790 TTTCAAAATC
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
29 9 0.24
30 28 0.76
ACGTcount: A:0.28, C:0.06, G:0.10, T:0.56
Consensus pattern (29 bp):
TTTATTTTTGTTAAGTTTAGTACATAAAC
Found at i:62987 original size:25 final size:24
Alignment explanation
Indices: 62949--62996 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
62939 ACGAAATGAT
62949 ATTAAAATAAAAAATGTTAAGTATA
1 ATTAAAATAAAAAAT-TTAAGTATA
*
62974 ATTAAAA-AATAAAATTTATGTAT
1 ATTAAAATAA-AAAATTTAAGTAT
62997 CAAAATAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (24 bp):
ATTAAAATAAAAAATTTAAGTATA
Found at i:63407 original size:7 final size:8
Alignment explanation
Indices: 63381--63406 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
63371 ACAATATTAA
63381 TTTATAAT
1 TTTATAAT
63389 TTTATAAT
1 TTTATAAT
63397 TTTATAAT
1 TTTATAAT
63405 TT
1 TT
63407 AAAAAATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (8 bp):
TTTATAAT
Found at i:64609 original size:12 final size:12
Alignment explanation
Indices: 64592--64621 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
64582 AGAGTAAAAT
64592 AAAAGAAAATAA
1 AAAAGAAAATAA
64604 AAAAGAAAATAA
1 AAAAGAAAATAA
*
64616 AGAAGA
1 AAAAGA
64622 TTAAAGAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.80, C:0.00, G:0.13, T:0.07
Consensus pattern (12 bp):
AAAAGAAAATAA
Found at i:64619 original size:21 final size:21
Alignment explanation
Indices: 64587--64638 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
64577 TGAAGAGAGT
64587 AAAATAAAAGAAAATAAAAAAG
1 AAAAT-AAAGAAAATAAAAAAG
* * *
64609 AAAATAAAGAAGATTAAAGAG
1 AAAATAAAGAAAATAAAAAAG
64630 AAAAGTAAA
1 AAAA-TAAA
64639 AGAATATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 17 0.65
22 9 0.35
ACGTcount: A:0.75, C:0.00, G:0.13, T:0.12
Consensus pattern (21 bp):
AAAATAAAGAAAATAAAAAAG
Found at i:64665 original size:12 final size:11
Alignment explanation
Indices: 64614--64666 Score: 52
Period size: 12 Copynumber: 4.5 Consensus size: 11
64604 AAAAGAAAAT
64614 AAAGAAGATTA
1 AAAGAAGATTA
* *
64625 AAGAGAAAAGTA
1 AA-AGAAGATTA
*
64637 AAAGAATATTA
1 AAAGAAGATTA
64648 AGAAGAAGATTTA
1 A-AAGAAGA-TTA
64661 AAAGAA
1 AAAGAA
64667 ATAAATTCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
11 10 0.29
12 20 0.59
13 4 0.12
ACGTcount: A:0.64, C:0.00, G:0.19, T:0.17
Consensus pattern (11 bp):
AAAGAAGATTA
Found at i:65403 original size:244 final size:244
Alignment explanation
Indices: 64972--65495 Score: 825
Period size: 244 Copynumber: 2.1 Consensus size: 244
64962 TCAATTTGCT
* ** **
64972 AAGTTGTTGACTAACTGCCACACCAGTATTTCATGCCCAAATTCATGCCTACTATTTTGGCCTTG
1 AAGTTGTTGACTAACTGTCACGTCAGTATTTCATGCCCAAATTCATGCCTACTATTCCGGCCTTG
* * *
65037 ATTCGAGAACAAAAAGTGTAATTTTTAGTCATTTTAAGCAAATTTTCCAAAAGTCATTGCGTTGC
66 ATTCGAGAACAAAAAGTGTAATTTTTAATCATTTTAAGCAAATTTTCCAAAAGTCATTACATTGC
*
65102 ACAAAAATCACGTACAAAGACCCAAATCAACAATAATAATTAACAAACGAAGAGTATTTAATCAT
131 ACAAAAATCACGTAAAAAGACCCAAATCAACAATAATAATTAACAAACGAAGAGTATTTAATCAT
* * *
65167 AAAATGTTGTCCAAAATAAACACTGAACGCTA-CTGAGTGGAGCTTCTAG
196 AAAATGTTGCCCAAAATAAACACTGAACGC-AGCTGAGTGAACCTTCTAG
* *
65216 AAGTTGTTGACTAACTGTCACGTCAGCATTTCATGCCCAAATTCATGCCTACTATTCCGGCCTTT
1 AAGTTGTTGACTAACTGTCACGTCAGTATTTCATGCCCAAATTCATGCCTACTATTCCGGCCTTG
*
65281 ATTCGAGAACAAAAAGTGTAATTTTTAATCATTTTAAGCACATTTTCCAAAAGTCATTACATTGC
66 ATTCGAGAACAAAAAGTGTAATTTTTAATCATTTTAAGCAAATTTTCCAAAAGTCATTACATTGC
** *
65346 ACCCAAATCACGTAAAAAGACCCAAATCAACAATAATAATTAACAAACGATGAGTATTTAATCAT
131 ACAAAAATCACGTAAAAAGACCCAAATCAACAATAATAATTAACAAACGAAGAGTATTTAATCAT
* *
65411 AAAATGTTGCCCAAAATAAACACTGAACGCAGTTGTGTGAACCTTCTAG
196 AAAATGTTGCCCAAAATAAACACTGAACGCAGCTGAGTGAACCTTCTAG
* * *
65460 AAGATGTTGATTCACTGTCACGTCAGTATTTCATGC
1 AAGTTGTTGACTAACTGTCACGTCAGTATTTCATGC
65496 TCACTGGTCC
Statistics
Matches: 255, Mismatches: 24, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
243 1 0.00
244 254 1.00
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (244 bp):
AAGTTGTTGACTAACTGTCACGTCAGTATTTCATGCCCAAATTCATGCCTACTATTCCGGCCTTG
ATTCGAGAACAAAAAGTGTAATTTTTAATCATTTTAAGCAAATTTTCCAAAAGTCATTACATTGC
ACAAAAATCACGTAAAAAGACCCAAATCAACAATAATAATTAACAAACGAAGAGTATTTAATCAT
AAAATGTTGCCCAAAATAAACACTGAACGCAGCTGAGTGAACCTTCTAG
Done.